I am able to use the clone stamp tool for all layers, smudge at any percentage with no black brush stroke. Can you attach your system information here from photoshop help>system info? Can you also give me the file your are having trouble with so I can see the issue first hand?

OK then. Other than the misunderstanding of the clone tool, are you still having trouble with the smudge tool at any other setting than 1%? If you are still having issues, please copy the information from Photoshop help>system info. It will tell us more than what you pasted in the above post.

The Smudge Tool appears to be passing the pixels repeatedly up through the layer pyramid, then re-depositing them on the image layer.

It's also very slow, as though the Brush Spacing isn't properly being done and is near zero. I even got it to virtually lock up with a 614 pixel brush. Definitely a bug there with the stroking of the Smudge Tool. I've seen it reported and discussed before, so it's possible Adobe will have that fixed by the release.

As far as what's going on with the color, though... One has to wonder: Of what use is the [ ] Sample All Layers checkbox when there's a stack of adjustments above the layer you're working on. What would you expect it to do?

Plus, it was probably designed to do so but I do not think it was to be so pronounced.

Exactly. It's as though the Smudge Tool is cycling through its process hundreds of times more than it should - kind of like what happens when the spacing value of a brush is set way too low. Notably the spacing value set in the Brush panel has no effect on the operation of the Smudge Tool.